Leave it to scientists to ruin all our long-held beliefs. First they told us that Santa Claus can't possibly give presents to all the good little boys and girls in the world [DOI: 10.1145/1132516.1132522], and now, they are telling us that penguins didn't always wear their iconic tuxedos.

According to an international team of researchers, a close examination of feathers from a recently unearthed giant penguin fossil revealed that it was clad in reddish-brown and grey, instead of the familiar black-and-white colors worn by its modern relatives. Additionally, the researchers found differences in feather structure between ancient and extant penguins; differences that may offer clues for how modern penguin feathers evolved.

The 36 million-year-old penguin fossil was discovered by a Peruvian undergraduate student, Ali Altamirano, on an expedition in Yumaque Point in the Paracas Reserve of Peru. The new species was dubbed Inkayacu paracasensis (EEN-kah-YAH-koo par-ah-kah-sin-sis) - from the local Native American language, Quechua, "Inka" for emperor and "yacu" for water; and the species name is paracasensis in honour of the Reserva Nacional de Paracas, where the specimen was found.

Based on measurements of the nearly complete skeleton (recovered bones are coloured white in Figure 1, below), Inkayacu's body length is almost 1.5 metres (5 feet) tall, making it one of the largest penguins to have ever lived - twice as big as the emperor penguin, Aptenodytes forsteri, the largest living penguin species. But like modern penguins, it hunted by diving for fish, as we can see from Inkayacu's long, grooved beak.

The specimen was recognised early on as being special because, unlike any other penguin fossils previously uncovered, this one was accompanied by imprints from surrounding soft tissues. When the team noticed the scaly soft tissue preserved on an exposed foot, Inkayacu earned the nickname "Pedro" after a sleazy (slang; "escamoso", which translates as "scaly") character in a Colombian soap opera.

In addition to the scales on its feet, careful preparation of Inkayacu also uncovered feathers that were preserved in exquisite detail. The feathers on the left wing were especially close to their real life position, appearing to be only slightly ruffled (Figure 2, below; A & B scale = 1 cm):

Several feather samples (red circles) were taken for scanning electron microscope (SEM) analysis (refer to the insets in Figure 2). As expected, the samples contained fossilised melanosomes. These are tiny sausage-shaped structures filled with pigments that are located inside cells. Melanosomes are nearly ubiquitous throughout the animal kingdom; providing a vast palette of colors to crustaceans, fish, amphibians, reptiles, mammals and birds.

Jakob Vinther, a co-author on the paper, used SEM to photograph the structure of the fossil penguin melanosomes and feathers. Mr Vinther, a graduate student at Yale University, studies ink sacs in fossil squids. He discovered the melanosomes in the fossil penguin feathers in 2008, shortly after he first noticed melanosomes in the feathers of another ancient bird fossil.

To identify the colours of the ancient feathers, team members Matthew Shawkey, an assistant professor of biology and integrated bioscience at the University of Akron, and Liliana D'Alba, a postdoctoral researcher who works with Dr Shawkey, compared the Inkayacu samples (Figure 3A and B) to similar structures in modern birds.

Dr Shawkey and Dr D'Alba have been constructing an encyclopedia of avian melanosomes for comparative purposes.

"My post-doc Liliana and I have built (and continue to build) a dataset of melanosome morphology from feathers of different colours," explained Dr Shawkey in an email. "This enables us to predict feather colour from morphology, which is very useful when you only have fossilised melanosomes to work with."

When they compared the fossil penguin melanosomes to those of modern penguins (Little Blue Penguin, Eudyptula minor, Figure 3C), they were in for a surprise.

"We thought the extant penguin melanosomes would fit right in with those from the other extant birds, but it turned out to be more interesting than that," said Dr Shawkey.

Although the fossil melanosomes are quite similar to those in modern birds, they are much smaller than those found in modern penguins, as you can see in the above figure (compare panels A and C in Figure 3).

Modern penguins' melanosomes are giants; much larger and broader than those found in the feathers of other living birds and in the fossil penguin feathers. The team also noted that their modern penguins' melanosomes are packed into clusters that resemble bunches of grapes, another feature that sets them apart from all other birds.

Comparisons with modern avian melanosomes of known coloration showed that each of the six Inkayacu samples most closely resembled modern bird melanosomes that were grey or reddish-brown. Interestingly, modern penguin chicks are either grey or a reddish-brown color. But the fossil bones are from an adult penguin, not a juvenile. According to Dr Shawkey, he and Dr D'Alba are investigating the feathers of penguin chicks now.

I asked Dr Shawkey if they have examined melanosomes from other largely aquatic birds.

"We've looked at loons and boobies and some ducks and they all fit in pretty well with the non-aquatic birds," said Dr Shawkey. "Of course, those aren't such prolific swimmers and divers as penguins."

I also wondered if they had examined melanosomes from another highly aquatic bird family, the auks - the northern hemisphere's "ecological equivalent" to penguins.

"We haven't looked at auks yet, although that's high on the list," said Dr Shawkey.

"Unfortunately I don't think we have any fossil auks preserved with feathers," added Mr Vinther. "But that is an interesting thing to pursue."

The researchers also noted structural differences in the feathers. Using these data, the researchers reconstructed a phylogenetic tree (Figure 4) for penguins on the basis of specific features of their melanosomes and feather structure (lack of differentiation between stacked remiges and greater coverts; densely packed, squamiform lesser coverts; and broad flattened contour feather rachises seen in extant penguins [insets]), all characters that appeared no later than the early Eocene, roughly 34m years ago.

The fossil record provides additional detail that was mapped onto this phylogenetic tree, showing that Inkayacu and other extinct giant penguins were very successful during the Eocene - they ranged all over the Southern Hemisphere (Antarctica: blue; New Zealand: green; Africa: dark gray; South America: red; in Figure 4).

"[This tree] tells us that after diverging roughly 34m years before Inkayacu, penguins were already pretty well adapted to aquatic flight [since their] heavy bones and modified feather shape are pretty much the same as modern penguins'," said Dr Shawkey. "However, their coloration clearly shifted, perhaps in response to the selection pressures imposed by new predators - especially seals - that emerged in the late oligocene (~23 mya)."

Modern penguins are counter-shaded so that they blend in with the light when seen from below and with the dark when seen from above, but clearly, Inkayacu was not. Was this lack of counter shading shared by all the giant penguins? If so, may this be the reason that all of the giant penguins are now extinct?

"By looking at the way these fossilised feathers differ from those of living penguins, we may be able to learn more about why species like Inkayacu became extinct, while the smaller modern species continue to survive today," said Daniel Ksepka, co-author on the paper and an assistant research professor of Marine Earth and Atmospheric Sciences at North Carolina State University.

But this phylogenetic tree does not reveal how or why penguin feathers changed over time. Part of that secret might lie in the odd shape of modern penguins' melanosomes.

"The hypothesis that we present [in the paper] is based on the fact that we know that melanosomes are involved not only in pigmentation but they also strengthen the feather," said Mr Vinther in an email message.

Feather strength is important, particularly when making a major life history transition from aerial flight to aquatic flight. Since penguins live in an environment where the substrate [water] is 800 times denser than air, their feathers are subject to a lot of wear and tear. Thus, it is possible that these modified melanosomes provide more strength to their feather.

"I consider a hydrodynamic explanation for the unusual melanosome shape, as indicated by Clarke et al, to be rather unlikely, as penguins have a white belly and often also a white underwing," remarked Gerald Mayr in an email message.

Dr Mayr, who was not involved in the study, is an expert in the palaeontology of birds at the Senckenberg Natural History Museum in Frankfurt am Main, Germany. He pointed out that, thanks to counter shading, half of modern penguin feathers are white and contain no melanosomes, yet they are subject to the same hydrodynamic forces as melanosome-rich black feathers.

"If there was a hydrodynamic function, penguins would probably have to be all black."

But Mr Vinther disagreed, pointing out that there are many selective pressures that must be balanced. "We know for example that seagulls have black wing tips but the rest of the bird is white," he said.

Obviously, penguins have a lot to teach us about how organisms evolve to meet the many different demands they are faced with.

"Insights into the colour of extinct organisms can reveal clues to their ecology and behavior," said Mr Vinther. "But most of all, I think it is simply just cool to get a look at the colour of a remarkable extinct organism, such as a giant fossil penguin."

Mr Jakob Vinther [email; 1 October 2010] (Mr Vinther, whose work I've followed for years, went to great lengths to share his thoughts with us because his right arm is confined to a plaster cast. His responses to my questions were interesting and at the same time, intensely amusing, due to the severe limitations of voice recognition software.)